I have a control system in which the co-crystal structure is determined. I would like to have rosetta only score the input pdb without docking, so that I can compare the crystal coordinates with the results. I would also like to be able to score the prepacked structure used for the actual studies.
I used the flag -run:score_only and this worked, but there was a score.sc file and a pdb file. Also, the rms was 30 in the score file. I re-ran and sure enough, the score was different, indicating that it is actually docking not merely scoring.
The flags I used were:
-extra_res_cen (because I have two heme proteins)
then -s protein.pdb
Is there another flag I should use for scoring a structure without docking it?